I3 and
> collect data at Cu wavelength for SAD phasing, which could help you to
> resolve the missing piece. Maybe.
> Cheers,
> Boaz
>
> Boaz Shaanan, Ph.D.
> Dept. of Life Sciences
> Ben Gurion University
> Beer Sheva, Israel
>
> On Nov 4, 2023 10:04, Sam Tang w
s spec of your crystal to identify the other protein. Once done
> solve your structure and build the complete model. This should be straight
> forward and quick.
>
> Best Wishes
>
> On Sat, 4 Nov 2023, 09:05 Sam Tang, wrote:
>
>> Dear community,
>>
>> I am solvin
Dear community,
I am solving the structure of a complex between proteins A and B, where A
is a protein with known homologs and B is a novel protein isolated from
plant. The diffraction data was at 1.9 Ang collected in-house, indexed to
P321. Using A as the search model, we have got a reasonable
Have just tried out some of the options -- done within minutes! Many thanks
for the numerous input!
All the best
Sam
On Wed, 29 Sept 2021 at 19:03, Sam Tang wrote:
> Dear community
>
> This may appear to be a silly question -- I am trying to add hydrogens to
> the structure in
Dear community
This may appear to be a silly question -- I am trying to add hydrogens to
the structure in PDB 1CDW. My initial thought is to run a single run of
refinement with a refinement program. It happens that I cannot locate the
map coefficients under the entry (am I missing something?)
Dear all
Sorry for an off-topic question here. I wonder if anyone may be aware of
any search program which allows one to 'blast' a protein domain just like
we 'blast' a protein sequence? For example I have an epitope in hand and
would like to find out whether this also exists in other proteins.
s*
>
> Senior Laboratory Research Scientist
>
> Signalling and Structural Biology Lab
>
> The Francis Crick Institute
>
> London, UK
>
> ==
>
> Diamond User Committee (MX)
>
> CCP4 WG2
>
> ==
>
> about.me/david_briggs
> --
Dear community
Sorry for an off-topic question here. I wonder if anyone may be aware of
any glycan modification database where we can predict what is what. For
example, if I got a mass difference of m/z X on LC-MS, and I would like to
have a rough idea what it might be, where should I go for?
Dear all
Thanks a lot for the numerous input. Will try the different strategies and
get back again soon.
BRs
Sam
On Thu, 1 Apr 2021 at 20:28, Sam Tang wrote:
> Dear all
>
> I have a dataset processed to 2.2 A, P212121, with no major issues
> identified by Xtriage (no tNCS,
Dear all
I have a dataset processed to 2.2 A, P212121, with no major issues
identified by Xtriage (no tNCS, no twinning, no ice ring, good
completeness). Phaser-MR gave a good solution except some loop regions are
shifted. There is only 1 molecule in the ASU (and seemingly no more
molecule can be
Hello fellow colleagues
Hope you are all well while the pandemics persists. I just wonder if anyone
may have an idea what this density (looking like a pentagon) might be. The
data was collected to 1.8 A and crystal was grown in Bis-tris + PEG3350.
Imidazole residual? Nucleotide (the protein
Hi
Not sure if it is the right place to go but I'm sure I can get some help
here. I am trying to combine two multi-state objects and save it to a new
object. It happens that the molecule is not correctly displayed after Save.
Would anyone have an idea what may have gone wrong?
ing
> all the DNA bases the same residue number. As you are using the old gui you
> might be able to do the same with pdbset or pdbcur, or maybe a graphics
> program.
>
> Cheers, Jon Cooper
>
>
> Sent from ProtonMail mobile
>
>
>
> Original Messa
Dear community
I ran PISA from CCP4i to analyze a protein-ssDNA complex with non-standard
modified nucleotides. It turns out that PISA identifies each nucleotide in
the DNA chain as a ligand (i.e. I have 7 DNA bases and PISA calls out 7
ligands). May I solicit your experience if there is a way to
Hi, the question may be a bit weird, but how do you define 'over-fitting'
in the context of structure refinement? From users' perspective the
practical aspect is to 'fit' the model into the density. So there comes
this question from our juniors: fit is fit, how is a model over-fit?
BRS
Sam
.b.coo...@protonmail.com
>
>
>
>
>
> Original Message
> On 16 Oct 2020, 06:57, Sam Tang < samtys0...@gmail.com> wrote:
>
>
> Dear all
>
> I attach herewith the Arg concerned. I actually saw no issue in Coot when
> I checked residue
ed side chain and a normal one?
>
> Best wishes, Jon Cooper. jon.b.coo...@protonmail.com
>
>
>
>
>
> Original Message
> On 15 Oct 2020, 15:07, Sam Tang < samtys0...@gmail.com> wrote:
>
>
> Dear colleagues
>
> I am trying to refine a s
Dear colleagues
I am trying to refine a structure with Refmac and the work completes
without any warning. However I am a bit puzzled for one single N atom on an
Arg residue the element type becomes N+1. This doesn't happen on my another
NCS chain and the input PDB seems fine. Could anyone kindly
Hi,
I'm going to install ccpEM on a same fedora 30 workstation that already has
ccp4 will they touch on my pre-existing Coot and Refmac setup?
Maybe I'm just worrying too much..?
Cheers
Sam
To unsubscribe from
Dear all
A very technical question which I believe a few simple mouse clicks would
solve. Is there a way I can ask Coot not to build the disulfide linkage
automatically (which lies within a strong red density)?
My WinCoot is version 0.8.9.2
Many thanks!
Regards
Sam
? In this case do you think refining at a (much) lower
resolution is acceptable?
Best regards
Sam
On Fri, 5 Jul 2019 at 13:43, Sam Tang wrote:
> Hello everyone
>
> Sorry for a naive question. Is there any circumstances where one may wish
> to refine to a lower resolution? For example if one h
Hello everyone
Sorry for a naive question. Is there any circumstances where one may wish
to refine to a lower resolution? For example if one has a dataset processed
to 2 A, is there any good reasons for he/she to refine to only, say 2.5 A?
Thanks!
Sam Tang
once for the low resolution data
>> and once for the high.
>>
>> Harry
>> --
>> Dr Harry Powell
>>
>>
>> --
>>
>> To unsubscribe from the CCP4BB list, click the following link:
>> https://www.jiscmail.ac.uk/cgi-bin/webadmin?SUBED1=CC
TERNAL] Re: [ccp4bb] High Rfree - ice ring
> >
> >
> > Dear Sam,
> >
> >
> >
> > I would remove the ice ring and reprocess the data. Ice rings may wreak
> havoc with scaling so at minimum you have to redo the scaling.
> >
> >
> >
than one copy per asymmetric unit, are you imposing NCS
> restraints during refinement?
>
> -Eric
>
>
>
> On Wed, Apr 3, 2019 at 1:41 PM Sam Tang wrote:
>
>> Hi everyone again
>>
>> Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
>> af
Hi everyone again
Hmmm I think we have solved a structure in P1 space, to 2.5 A. However
after refinement the Rfree stuck at 33%-35% with Rwork around 26%. The
structure was solved by MR and current model seems to fit density well. In
Refmac log I found that at the resolution corresponding to
Hi
My apologies. This is indeed a silly question. It appears I forgot to
remove the extra O when linking them together!
Sam
On Wed, 3 Apr 2019 at 07:21, Sam Tang wrote:
> Dear all
>
> Hello again.
>
> We have another protein-RNA dataset which we are trying to refine. For
&g
Dear all
Hello again.
We have another protein-RNA dataset which we are trying to refine. For this
dataset we have three OMU nucleotides modelled. We got the monomer from
Coot 'Get Monomer'. Refmac returned the following error:
ERROR : atom :OP3 OMU 2 CCC is absent in the
Hello
I have been refining a protein-RNA complex with Refmac. The RNA we used was
tagged with a Cy label. I modelled the RNA in Coot using the RCrane add-on
and manually built the Cy tag. However after Refmac (also via Coot) the
linkage between Cy and the RNA was always broken.
I guess I must
Dear all
Thanks for all the input both on- and off- the list. We shall definitely
look into these suggestions further and report again here in due course.
Kind regards
Sam
On Tue, 9 Oct 2018 at 19:12, Sam Tang wrote:
> Dear all
>
> Hello. We recently shot a crystal (a protein w
...@diamond.ac.uk <
colin.n...@diamond.ac.uk> wrote:
> Sam
>
> Would this unit cell index some of the spots?
>
> a = 7.00 ± 0.04 A, b = 9.96 ± 0.05 A, c = 6.29 ± 0.04 A.
>
> Colin
>
>
>
> *From:* CCP4 bulletin board *On Behalf Of *Sam
> Tang
>
To add to the discussion, could I raise a relevant question about
generating ESP (Apologies to Jiri if this distracts too much from your
initial thread).
In our structure in hand, the density for two conformations of the side
chain are clearly seen and they could be modeled. This brings a bit of
Dear all
Sorry for the slightly off-topic thread.
We are lucky enough to have recently solved a protein-ligand structure in
P1 space to 2.4 A by molecular replacement using the apo-protein as model.
The protein is known to have a flexible loop region of about 20 amino acid
long. In the
, Paul Emsley <pems...@mrc-lmb.cam.ac.uk> wrote:
> On 24/01/2017 08:04, Sam Tang wrote:
>
>>
>> I am trying to fit a small molecule ligand into a protein complex using
>> Coot. The data was
>> processed to P212121, at 2.6 A. What I did was to input a SMILES
(Also, the chain ID O was identified as OO?) In a
test run I carried out rigid body refinement and the programme finished
without issues.
Is there a way I could rectify the above problem? Thanks in advance for
your attention and input.
Kind regards
Sam Tang
Biochemistry Programme, School of Life Sciences, CUHK
at the other. In the P6 case, the RNA ligand (in the
> center of a hexameric protein) was rotationally averaged, but in the P1
> case it could be resolved.
>
> Best wishes
> Kevin
>
> On Fri, Oct 28, 2016 at 6:13 AM, Sam Tang <samtys0...@gmail.com> wrote:
>
>>
that there is
no twinning), ~2.5 Angstrom
Xtal2: P1 (53 60 79 106 105 98), ~3 Angstorm
Would it be possible that the ligand changes the SG of the crystal so that
only one of the forms contains the ligand?
Any advice is appreciated and thanks a lot in advance for your input.
Regards
Sam Tang
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